The club have confirmed that the England international sustained "slight damage to his posterior abdominal wall" prior to their 3-1 victory at the Emirates Stadium.
It means that the winger will miss two Premier League games as well as ties in the League Cup and UEFA Champions League, with 24-year-old also set to be absent for England's FIFA World Cup qualifiers against Montenegro and Poland in October.
However, manager Arsene Wenger is confident that Walcott will be able to begin his rehabilitation soon after the procedure.
"Theo will be out for a few weeks," Wenger told Arsenal's official website. "He has developed some damage to his posterior abdominal wall. It's not a hernia, but it's a little structural problem in his abdomen.
"He will have the procedure in Germany on Wednesday and, because it's so minor, we can begin his rehab immediately.
"We are pleased it's being dealt with quickly and he shouldn't miss too many Arsenal matches. But he will miss the forthcoming international matches with England."
Walcott has made four appearances for Arsenal in the Premier League this season but is yet to score domestically.
